Rob Beagrie

One frame. Many voices. ✨
This International Women’s Day, our Women in Science series features group leader Christa Bücker 🙌

Today, @chribue.bsky.social shares an important perspective on finding role models and becoming one for the next generation 👩‍🔬

@univie.ac.at
@meduniwien.ac.at

This is a common reply to concerns about GenAI research as if it were just another computational tool that saves us times from tedious tasks and whose accuracy can be rigorously quantified.

It is not.

GenAI research poses at least 2 serious problems... /n

A screenshot of genome browser tracks showing the chromatin interactions made by the Sox2 promoter over around 30 Mb. When FACT levels are normal, no interaction is detected between Sox2 and the adjacent genes Fxr1, Atp11b and Tiparp. When FACT is depleted, strong new interactions form between Sox2 and Fxr1, Sox2 and Atp11b and Sox2 and Tiparp.

Ana shows that degradation of the histone chaperone FACT causes nucleosome loss at active gene promoters and spreading of chromatin binding factors into gene bodies. New ultra-long promoter-promoter interactions also form, including this mammoth one between Sox2 and Tiparp that spans nearly 30 Mb!

A pictographic model of chromatin folding in the nucleus. DNA wrapped around nucleosomes aggregates into nanoscale domains, whilst newly nucleosome depleted DNA that forms after acute degradation of FACT projects from these domains and engages in long-range interactions that can span TAD boundaries

New preprint from @anadopico.bsky.social (who I have had the great pleasure of supervising with Tom Milne) and our fantastic collaborators in the @davieslab.bsky.social

www.biorxiv.org/content/10.6...

#genomics #GeneRegulation #chromatin

I am excited to share a new review @cp-molcell.bsky.social written in collaboration with @tanjamittag.bsky.social , Mikayla Eppert, and Ambuja Navalkar where we review the current evidence for and against the role of density transitions in regulating transcription www.cell.com/molecular-ce...

New preprint from the lab! We dig into the regulatory roles of TEs in the mouse placenta, with some surprising findings. Led by the awesome @smamante.bsky.social. Particular kudos to him for navigating the many twists and turns of the project.

This is probably my favorite paper of 2025. Beautiful work by @elphegenoralab.bsky.social and @karissalhansen.bsky.social that should be on the top of the reading list for everyone with even a slight interest in gene expression!

“It is not acceptable to recruit a variety of students into the laboratory, subject them to a variety of stress tests and abuses, and then keep the students who thrive under abuse and get rid of the students who aren't able to thrive in the lab. That's straight-up exploitation.”

👏👏👏

Last few days to apply for this PhD project in our lab. Mix of biochemistry and structural biology, DNA replication and ubiquitin signalling. Get in touch if interested. Full application through official university portal. Deadline on 27th of November!

Our latest paper has just been published in Cell!

doi.org/10.1016/j.ce...

We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.

don't release preprints without a Methods section
don't release preprints with a Supplementary Materials section
don't release preprints without data
don't release preprints without code

use preprint servers to share your science, not advertisements

(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen!

Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵

New paper on the role of H3K4me3 at enhancers! We (led by Haoming Yu) used dCas9 epigenome editing to add H3K4me3 to intergenic enhancers. This was (1) sufficient to turn up transcription at open, active regions and (2) has no effect on target gene transcription. genesdev.cshlp.org/content/earl...

Most people I know are doing PE150 because it almost always ends up cheaper if you’re outsourcing. But I’d be interested to know how much fragment size affect mappability. Presumably the larger the fragment the better the chances of at least one end having a unique alignment?

Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells - Nature Communications Here the authors show that reducing enhancer-promoter distance at the Pitx1 locus increases proportion of Pitx1 forelimb expressing cells, worsening skeletal defects in Liebenberg syndrome. They also ...

Our work bridging enhancer-promoter proximity to phenotypic outcomes in vivo is out! Shout out to @olimpiabompadre.bsky.social, to Marie Kmita's lab, and to all the co-authors. www.nature.com/articles/s41...

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Maternal iron deficiency causes male-to-female sex reversal in mouse embryos - Nature Iron-deficient conditions in pregnant mice can cause XY mouse embryos to develop female rather than male genitalia, revealing that iron metabolism has a role in determining male sex in mice.

This is the type of transgender mouse research that would get its money stripped away in the US... (jk jk) www.nature.com/articles/s41...

Extensive differences observed in 3D genome structure between homologous heterozygous chromosomes revealed by Genome Architecture Mapping #GAM in the @apombo1.bsky.social lab ➡️ www.embopress.org/doi/full/10....

Systematic identification of disease-causing promoter and untranslated region variants in 8040 undiagnosed individuals with rare disease #RareDisease #Genetics genomemedicine.biomedcentral.com/articles/10....

Reversible histone deacetylase activity catalyzes lysine acylation - Nature Chemical Biology Tsusaka et al. discover that histone deacetylases, which are well known to remove protein modifications, such as lysine acetylation and β-hydroxybutyrylation, can also reverse their chemical activity ...

My favorite science is the kind that makes you says, "Man, I wish I thought of that!" This is such a paper.

Mass action turns an eraser into a pen. HDACs are metabolite-dependent histone acyltransferases.

@dremilygoldberg.bsky.social @gburslem.bsky.social

www.nature.com/articles/s41...

Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,...

A really nice paper by @drghawkes.bsky.social et al. argues that rare and common genetic associations converge on the same genes.

While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)

www.biorxiv.org/content/10.1...

Delighted to have been able to help out with this project - congratulations Ali and the rest of the @drakesmith-lab.bsky.social - such a fascinating #genetics and #GeneRegulation story 🧪

This is going to be such a disaster. Cis-women will be outed as trans for genetics they had no idea about. What then?

Pet peeve: I hate how often ppl claim “all the researchers will just move to Europe/Canada!” You vastly under-estimate how little money there is there vs the USA- and unless that changes ASAP this loss is just going to decimate global science, full stop. 🧪🔭

I wrote up some thoughts on the idea of recruiting embattled American scientists to Europe. My main point: it would work best to keep the talent pipeline going, but not to salvage individual careers, especially mature ones. The barriers are many.

michaelerard.com/blog/a-few-t...

My son Charlie — and the breakthrough that changed our lives James Coney and his wife, Sarah, struggled not knowing why their 12-year-old was born with a severe learning disability. In their darkest moments, they blamed themselves. Then, out of the blue, came a...

A few weeks ago, I had an incredibly emotional call with James Coney, a writer for the Sunday Times whose son Charlie was in the @genomicsengland.bsky.social 100k project and was recently diagnosed with ReNU syndrome. This beautiful article tells their story ❤️ www.thetimes.com/article/0bcc...

Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr…

Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development.

Loss of a single CTCF motif is sufficient to cause embryonic lethality.

www.sciencedirect.com/science/arti...

Preeclampsia risk prediction from prenatal cell-free DNA screening - Nature Medicine Using 1,854 routinely collected clinical samples from early in pregnancy, with validation in an external cohort, low-coverage cfDNA sequence data identified distinctive features among those who developed preeclampsia.

Prenatal DNA screening successfully predicts preeclampsia risk early in pregnancy, identifying tissue dysfunction months before onset.

by Adil M, Kolarova TR (...) Shree R et 15 al. in Nat Med #MedSky

📖 read the article:

The Marzi Lab in epigenetics band t-shirts

📢 Our lab is looking for a bioinformatics postdoc. We have lots of exciting projects to work on, including single cell (epi-)genomics, microglia xenotransplantations and nanopore long reads splicing analysis. Look out for the official advert next week and get in touch in the meantime 🧬🧠

Reminder of an exciting conference 'Hidden Cell, Dark Genome', Edinburgh 3-4th April 2025!

Sessions:
• Regulatory functions of the dark genome
• Uncharted proteins and RNA complexity
• Cellular diversity
• Atomic structures at the cellular scale

Early bird and registration deadline: 28th February!